The end of the story of Isa AS is shrouded in controversy between the Muslims and the Christians. Apart from the concept of the trinity (which is strongly refuted in Muslim scriptures), Christian doctrines claim that Isa AS was crucified: to the extent that the cross or the crucifix is accepted as the symbol of Christianity. According to the Muslim teachings, Isa AS was neither killed nor crucified, but was raised to heaven.
There are several accounts of how the attempt on Isa's AS life took place. In one version, the king of the time commanded that Isa AS be killed, and one of the disciples, Judas Iscariot, betrayed Isa AS and revealed his whereabouts to the king's men. As a punishment, Allah transformed his features so that he resembled Isa AS, and he was the one who was arrested and crucified instead. In another version, when the king's men entered the house where Isa AS was in, Isa AS asked his disciples which of them would like to bear his likeness and be killed in his place, upon which one of his disciples volunteered and was crucified in his place. There are other versions of the story, but there is no single authenticated version under Hadith or Qur'an.
What is certain is that Isa AS was neither killed nor crucified, but someone else was made to bear his likeness. This is clearly stated in the Qur'an:
"And [for] their saying, "Indeed, we have killed the Messiah, Isa, the son of Maryam, the messenger of Allah." And they did not kill him, nor did they crucify him; but [another] was made to resemble him to them. And indeed, those who differ over it are in doubt about it. They have no knowledge of it except the following of assumption. And they did not kill him, for certain." (Al Qur'an 4:157)
Instead of crucifixion, the Qur'an confirms that Isa AS was raised to Allah:
"Rather, Allah raised him to Himself. And ever is Allah Exalted in Might and Wise." (Al Qur'an 4:158)
"[Mention] when Allah said, "O Isa, indeed I will take you and raise you to Myself and purify you from those who disbelieve and make those who follow you [in submission to Allah alone] superior to those who disbelieve until the Day of Resurrection. Then to Me is your return, and I will judge between you concerning that in which you used to differ." (Al Qur'an 3:55)
Given that Muslims believe that the Qur'an is the word of Allah, we consider the subject closed and not worthy of any further debate. In particular, there is no advantage in relying and refuting contrary beliefs based on Christian scriptures, as the Qur'an has the overriding and final say on this subject, and as Muslims, we are not to accept any other information that contradicts with the word of the Almighty.
What Happened to the Message?
Over the centuries, the message of Isa AS steadily distorted, and when combined with the existing corruption already done by the scholars of Bani Israel to the Taurat and Zabur, the message of Islam became corrupted. Fundamental notions of the Almighty's Oneness were openly contradicted through the concept of Isa AS being the son of God, and also the concept of the trinity: these deviations challenge the very root of Allah's Oneness and His attributes and are an abomination of the original message of Islam.
The teachings of Isa AS were subsequently consolidated with the previous scriptures, but these were intermingled with the existing lies and falsehood propagated by Bani Israel to the divine message. The origins of the Bible in its present form cannot be authoritatively traced back to the time of Isa AS, although some Christian historians assert that the form of the Bible available today was compiled 100 to 600 years after the supposed crucifixion of Isa AS.
This phenomenon is already described in the Qur'an:
There is among them a section who distort the Book with their tongues: (As they read) you would think it is a part of the Book, but it is no part of the Book; and they say, "That is from Allah," but it is not from Allah: It is they who tell a lie against Allah, and (well) they know it! (Al Qur'an 3:78)
They (Jews and Christians) took their rabbis and their monks to be their lords besides Allah (by obeying them in things which they made lawful or unlawful according to their own desires without being ordered by Allah), and (they also took as their Lord) Messiah, son of Maryam, while they (Jews and Christians) were commanded [in the Taurat (Torah) and the Injeel (Gospel)) to worship none but One Ilah (God - Allah) La ilaha illa Huwa (none has the right to be worshipped but He). Praise and glory be to Him, (far above is He) from having the partners they associate (with Him)." (Al Qur'an 9:31)
This is nothing new, which is why Allah has repeatedly sent Prophets and Messengers to different communities in order to correct them every time they deviated from the message.
In the case of Isa AS, only one subsequent Prophet was sent to correct these deviations, this time to the entire mankind instead of the community of Bani Israel specifically. The guidance is through the Qur'an, which completed the message of the previous holy scriptures, and the messenger is Muhammad SAW:
And this Quran is not such as could ever be produced by other than Allah (Lord of the heavens and the earth), but it is a confirmation of (the revelation) which was before it [i.e. the Taurat (Torah), and the Injeel (Gospel), etc.], and a full explanation of the Book (i.e. laws and orders, etc, decreed for mankind) - wherein there is no doubt from the Lord of the 'Alamin (mankind, jinns ,and all that exists). (Al Qur'an 10:37)
In the case of the Qur'an, there is only one single version in existence. There is no deviation at all, no matter which part of the world the Qur'an is located and which century it was published. The only differences are in the translation and the interpretation, but it is unanimously agreed that there is only one version of the Qur'an, which has not changed by a single letter since the time it was revealed over 1400 years ago.
The Qur'an warns:
Indeed, We sent down the Taurat (Torah), in which was guidance and light. The prophets who submitted [to Allah] judged by it for the Jews, as did the rabbis and scholars by that with which they were entrusted of the Scripture of Allah, and they were witnesses thereto. So do not fear the people but fear Me, and do not exchange My verses for a small price. And whoever does not judge by what Allah has revealed - then it is those who are the disbelievers. (Al Qur'an 5:44)
That aside, the deviation of the priests and rabbis from the original message of Allah is already mentioned in the Qur'an, together with a warning on their fates:
O you who have believed, indeed many of the scholars and the monks devour the wealth of people unjustly and avert [them] from the way of Allah. And those who hoard gold and silver and spend it not in the way of Allah - give them tidings of a painful punishment. (Al Qur'an 9:34)
We can see live examples of these, and the abuse and corruption of the teachings of Christianity and its message. However, like many of the religions, it is not the original doctrine that is the issue, but the corruption of man that has tainted the original message.
The Second Coming
The story of Isa AS is unique in one final sense: it is not over yet. All other Prophets and Messengers (including Rasulullah SAW) have passed away after the completion of their missions, and their time on earth is over. In the case of Isa AS, he will, close to the end of the world, descend back to the earth to complete his mission, which is to defeat the Dajjal (the Antichrist) and to lead the Muslims in waging a final battle against the disbelievers and restoring peace on earth. He will then, like the rest of his prophets in brotherhood, die a natural death.
All this lies in the realms of the unknown, but have been prophesised in various ahadeeth. In part of one long hadith on the end of time, the Messenger of Allah (SAW) said, "Dajjal (the Antichrist) will appear in my Ummah and he will stay in the world for forty. I do not know whether this will be forty days or forty months or forty years. Allah will then send Isa, son of Maryam. Isa will pursue him and slaughter him. Then people will survive for seven years (i.e., after the demise of Isa) in the state that there will be no rancour between two persons." (Bukhari)